Biological soil crusting (BSCs) plays an important ecological function in water and soil retention, nutrient resupply in the Loess Plateau. Nitrogen fixing microorganisms are the key functional group for soil nitrogen fixation process and affect the soil N balance, however, the severe soil loss in the hydro erosive and erosive staggered zones of the Loess Plateau resulted in substantial loss of soil nutrients, especially N. BSCs develop widely in this region, and they play an important role in the process of nitrogen accumulation in soils in arid semi-arid regions. But the nitrogen fixation potential, diversity of nitrogen fixing microbial community and its key environmental control factors in different developmental stages of biological nodulation in this region are still unclear. Here, we used the Illumina hiseq platform to perform bioinformatics analysis of the amplified products of the nifH gene to reveal the distribution pattern of the nitrogen fixation potential and diversity of the microbial community, using the loess plateau water cavitation interlace as the research area, three biological crusting types and nude ground controls. The results showed that the BSCs succession significantly changed the nitrogenase activity (NAc), nifH gene abundance, and α-diversity of diazotrophs, while these parameters were significantly higher in moss crusts than those in bare soil, light and dark algal crusts, and lichen crusts. They also showed higher values in 0-2 cm biocrust layer than those in subsurface soil below BSCs. Diazotrophic community in bare soil was dominated by Rhodospirillales, Acidithiobacillales, and Rhizobiales of phylum Proteobacteria. Nostocales belonging to Cyanobacteria were the dominant diazotrophs in algal crusts, lichen crusts, and moss crusts. Trichormus and Nostoc were keystone species in Nostocales. However, compared with algal crusts and lichen crusts, the relative abundance of Nostocales significantly decreased and the relative abundance of Rhodospirillales, Acidithiobacillales, and Rhizobiales increased in moss crusts. Besides that, Cyanothece, Anabaena, Skermanella, Ruminclostridium were also dominant in algal crusts, lichen crusts, moss crusts. The relative abundance of Nostocales and Trichormus represented significant and positive correlations with nitrogenase activity and nifH gene abundance, while it was negatively correlated with Rhodospiraceae, Acidobacteria, Clostridiales and Rhizobiales; indicating that Trichormus might play key role in N inputs in BSCs on the Loess Plateau. The variations of physicochemical properties, including soil pH, organic matter, total nitrogen, water content caused by biological crust succession, altered the microhabitat, and exerted a comprehensive regulation on the diazotrophic community through environmental screening. Among soil physicochemical properties, pH and TN played critical role in regulating diazotrophic community.